Fig. 6

Analysis of residual plasma viruses on effective ART in Pt-2. Maximum likelihood phylogenetic tree (unrooted) of the plasma, proviral, and episomal viral variants detected 12 weeks after switching treatment. a Plasma viremia sequences (gold) and episomal vDNA from PBMCs (violet) are highlighted. Predominant plasma clusters and episomal clusters are identified, and the proportion of sequences included (in percentages) are indicated. In the same tree, color shading identify branches containing >10 % of the proviral sequences from each subset. The overall distribution of proviral versus episomal sequences are shown in (b) and (c), respectively, color-coded according to the CD4⁺ T-cell subset they come from. In all trees, the overall result from the Env-tropism prediction is indicated